Pluripotency factors determine gene expression repertoire at zygotic genome activation

Meijiang Gao,Anna Gebhard,Helge Hass,Sergey V Ulianov,Aileen Julia Riesle,Daria Onichtchouk,Jens Timmer,Lenka Buryanova,Marina Veil,Lev Y Yampolsky,Björn Grüning,Marcus Rosenblatt

doi:10.1038/s41467-022-28434-1

Abstract

Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that two factors modify chromatin in a largely independent manner. We distinguish four types of direct enhancers by differential requirements for Pou5f3 or Sox19b. We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of Pou5f3 and Sox19b leads to premature expression of genes, involved in regulation of organogenesis and differentiation.

Highlights

Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors
midblastula transition (MBT) is characterized by cell cycle lengthening, loss of cell synchrony, activation of zygotic transcription, and appearance of cell motility[31]
Gene expression starts as a result of a multi-step regulatory program involving a rapid succession of changes in chromatin accessibility, histone modifications, and transcription[65]

Summary

Introduction

Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. We analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. TFs that broadly activate zygotically expressed genes have been identified in Drosophila[7], zebrafish, Xenopus, and mammals[8]. Zygotic transcription is activated by homologs of mammalian pluripotency factors: Pou5f3, Sox19b, and Nanog in zebrafish[9,10], Pou5f3 and Sox[3] in Xenopus[11]. Reduction or loss of genome-activating TFs in Drosophila, zebrafish, and Xenopus resulted in the decreased chromatin accessibility on their binding sites[13,14,15,16]. Mammalian POU5F1 and SOX2 reprogram somatic cells to pluripotency and are in several cases sufficient for reprogramming[21]

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